4OVK

Crystal structure of periplasmic solute binding protein from Veillonella parvula DSM 2008

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.146	α = 90
b = 58.872	β = 90
c = 113.751	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.72	50	99.5	0.086	18.4	7	40447	38941		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.73	100		0.923		6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.71	25.76	37464	1883	94.66	0.142	0.1395	0.1881	RANDOM	24.3013

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.1			1.93		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.665
r_dihedral_angle_2_deg	38.565
r_dihedral_angle_4_deg	22.872
r_sphericity_bonded	19.817
r_dihedral_angle_3_deg	12.633
r_dihedral_angle_1_deg	5.183
r_rigid_bond_restr	1.634
r_angle_refined_deg	1.176
r_angle_other_deg	0.745
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.665
r_dihedral_angle_2_deg	38.565
r_dihedral_angle_4_deg	22.872
r_sphericity_bonded	19.817
r_dihedral_angle_3_deg	12.633
r_dihedral_angle_1_deg	5.183
r_rigid_bond_restr	1.634
r_angle_refined_deg	1.176
r_angle_other_deg	0.745
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2627
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.